EP3207159A2 - Adn de conversion de séquence et amplificateur de signal comportant des séquences espaceurs de poly-adn et procédés de détection l'utilisant - Google Patents

Adn de conversion de séquence et amplificateur de signal comportant des séquences espaceurs de poly-adn et procédés de détection l'utilisant

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Publication number
EP3207159A2
EP3207159A2 EP15850183.3A EP15850183A EP3207159A2 EP 3207159 A2 EP3207159 A2 EP 3207159A2 EP 15850183 A EP15850183 A EP 15850183A EP 3207159 A2 EP3207159 A2 EP 3207159A2
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EP
European Patent Office
Prior art keywords
dna
sequence
nucleic acid
oligonucleotide
signal
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
EP15850183.3A
Other languages
German (de)
English (en)
Other versions
EP3207159A4 (fr
EP3207159B1 (fr
Inventor
Ken Komiya
Makoto Komori
Toru Yoshimura
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Tokyo Institute of Technology NUC
Abbott Laboratories
Original Assignee
Tokyo Institute of Technology NUC
Abbott Japan Co Ltd
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Publication of EP3207159A2 publication Critical patent/EP3207159A2/fr
Publication of EP3207159A4 publication Critical patent/EP3207159A4/fr
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Publication of EP3207159B1 publication Critical patent/EP3207159B1/fr
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/682—Signal amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions

Definitions

  • PCR polymerase chain reaction
  • the following disclosure provides alternative methods and compositions for detecting a nucleic acid sequence (such as DNA or RNA) under reaction conditions that are less rigorous than those used in PCR.
  • the methods and compositions maintain sequence selectivity and sensitivity that allows for the detection of nucleic acid molecules that may be in a sample at low concentrations and/or nucleic acid molecules of a short length.
  • the methods and compositions also reduce reaction times.
  • the disclosure provides novel methods and nucleic acid molecules that can improve the detection limit of target nucleic acids in a sample under low temperature, isothermal conditions, and can simplify or improve sample preparation and automated methods of detection, while decreasing reaction times.
  • the disclosure relates to a method for detecting a target nucleic acid in a sample, said method comprising contacting said sample with: an oligonucleotide (sequence conversion DNA or SC DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer sequence (PDS), and a sequence (C) complementary to the 3' end of a target nucleic acid; a polymerase; and an endonuclease for a nicking reaction.
  • the method also comprises determining the presence or absence of a signal DNA, wherein the presence of the signal DNA indicates the presence of the target nucleic acid in the sample.
  • the disclosure relates to a method for detecting a target nucleic acid in a sample, said method comprising contacting said sample with: a first oligonucleotide (sequence conversion DNA or SC DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer sequence (PDS), and a sequence (C) complementary to the 3' end of a target nucleic acid; a second oligonucleotide (signal amplifier DNA or SA DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (D) that is homologous to the signal DNA generation sequence (A) of the first oligonucleotide, an endonuclease recognition site (E) (which may be the same or different from the endonuclease recognition site (B) in the SC DNA), a poly DNA spacer sequence (PDS) (which may be the same or
  • the method also comprises determining the presence or absence of a signal DNA, wherein the presence of the signal DNA indicates the presence of the target nucleic acid in the sample.
  • the signal amplifier DNA SA DNA
  • PDS poly DNA spacer sequence
  • the spacer is a poly "nucleic acid" spacer, and for example can be a poly DNA spacer (PDS), a poly RNA spacer (PRS), or a derivative or analog thereof (e.g., artificial nucleic acid).
  • the poly DNA spacer (PDS) sequence may comprise G, A, T, C, or any combination thereof.
  • the poly RNA spacer (PRS) sequence may comprise G, A, U, C, or any combination thereof.
  • the PDS sequence can be from 1 to 20, from 1 to 15, from 1 to 10, from 1 to 8, from 1 to 6, or from 1 to 5 bases long.
  • RNA - DNA hybrid duplexes As described in greater detail below, methods disclosed herein are especially useful for the detection of target RNAs in a sample.
  • the placement in a SC DNA of a poly DNA spacer (PDS) sequence between the endonuclease recognition site (B) and the sequence (C) complementary to the 3' end of a target greatly enhances the rate at which signal DNA is generated.
  • the disclosure relates to the acceleration or enhancement of endonuclease nicking activity downstream from, upstream from, and/or adjacent to RNA - DNA hybrid duplexes.
  • the polymerase may have strand displacement activity.
  • the polymerase may be 3' to 5' exonuclease deficient, 5' to 3' exonuc lease deficient, or both 3' to 5' exonuclease deficient and 5' to 3' exonuclease deficient.
  • the polymerase comprises a DNA polymerase.
  • the endonuclease may comprise a nicking endonuclease or a restriction endonuclease that can be used in a reaction that nicks an oligonucleotide.
  • the method disclosed herein may be performed under typical DNA amplification conditions (e.g., typical temperatures associated with standard PCR, reactant concentrations, time cycles, etc.), in some embodiments the method may be performed under isothermal conditions or under substantially constant temperatures. In further embodiments the method may be performed at temperatures that are lower than temperatures used in standard PCR methods. As one example, some embodiments of the method may be performed at a temperature at or below a calculated optimal hybridization or annealing temperature, or an experimentally determined hybridization or annealing temperature, of the target nucleic acid (T) and the sequence (C) of the SC DNA, or of the signal DNA (S) and the sequence (F) of the SA DNA as described below.
  • T target nucleic acid
  • C sequence
  • S signal DNA
  • F signal DNA
  • the method may be performed at a temperature that is below the melting temperature of the target nucleic acid (T) bound to the sequence (C) of the SC DNA, or the signal DNA (S) bound to the sequence (F) of the SA DNA.
  • the method may be performed at temperatures that allow for polymerase and/or endonuclease activity.
  • the method may be performed at temperatures that are at or about the optimal reaction temperature for the polymerase and/or endonuclease present in the reaction mixture for the detection of a target nucleic acid in a sample.
  • the disclosure relates to an oligonucleotide, which may be referred to herein as a “signal amplifier DNA” (or “SA DNA”) comprising, in the 5' to 3' direction, a signal DNA generation sequence (D) homologous to a signal DNA generation sequence (A) of a sequence conversion DNA (SC DNA), an endonuclease recognition site (E), a poly DNA spacer (PDS) sequence, and a sequence (F) which is homologous to a signal DNA generation sequence (A) of a sequence conversion DNA (SC DNA).
  • SA DNA signal amplifier DNA
  • the disclosure relates to signal amplifier DNA comprising, in the 5' to 3' direction, a signal DNA generation sequence (D) homologous to a signal DNA generation sequence (A) of a sequence conversion DNA (SC DNA), an endonuclease recognition site (E), and a sequence (F) which is homologous to a signal DNA generation sequence (A) of a sequence conversion DNA (SC DNA).
  • D signal DNA generation sequence
  • A signal DNA generation sequence
  • SC DNA sequence conversion DNA
  • E endonuclease recognition site
  • F which is homologous to a signal DNA generation sequence (A) of a sequence conversion DNA (SC DNA).
  • the SC and/or SA DNAs of the present disclosure are generally linear, however these DNAs can also be circular (i.e. mini-circle DNA (mc)).
  • Rolling circle amplification (RCA) can be primed upon binding of the 3 ' end of a target nucleic acid to a mini-circle SC DNA, or upon binding of the 3 ' end of a signal DNA to a mini-circle S A DNA.
  • the resulting RCA product is a long single-stranded DNA fragment containing thousands of copies of the SC DNA or SA DNA.
  • the signal DNA generation sequence (A) of a SC DNA can be complementary to the 5 '-end of a target nucleic acid (T).
  • any one of the signal DNAs produced in accordance with the methods disclosed herein can serve as a primer in a rolling circle amplification reaction.
  • the 3' end of a signal DNA produced according to methods of the present disclosure can be complementary to a mini-circle DNA template, and rolling circle amplification can be initiated upon binding of the signal DNA.
  • the target nucleic acid sequence may be any nucleotide sequence of interest and in some embodiments may comprise a sequence that originates from an infectious agent or a micro-RNA. In other embodiments the target nucleic acid may comprise a sequence from a gene that may be associated with a disease or a disorder.
  • the endonuclease recognition site comprises a sequence that is complementary to a sequence that is nicked by an endonuclease.
  • the sequence that is nicked by the endonuclease is adjacent (downstream or upstream) to the sequence that is specifically recognized by the endonuclease.
  • the disclosure relates to a composition for detecting a target nucleic acid in a sample, said composition comprising: an oligonucleotide (sequence conversion DNA or SC DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer (PDS) sequence, and a sequence (C) complementary to the 3' end of a target nucleic acid; a polymerase; and an endonuclease for a nicking reaction.
  • an oligonucleotide sequence conversion DNA or SC DNA
  • the disclosure relates to a composition for detecting a target nucleic acid in a sample, said composition comprising: a first oligonucleotide (sequence conversion DNA or SC DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer (PDS) sequence, and a sequence (C) complementary to the 3' end of a target nucleic acid; a second oligonucleotide (signal amplifier DNA or SA DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (D) that is homologous to the signal DNA generation sequence (A) of the first oligonucleotide, an endonuclease recognition site (E) (which may be the same or different from the endonuclease recognition site (B) in the SA DNA), a poly DNA spacer (PDS) sequence (which may be the same or different from
  • compositions can also comprise a polymerase, and/or an endonuclease capable of nicking at or adjacent to the endonuclease recognition site of the first and second oligonucleotide when the endonuclease recognition site is double stranded.
  • Compositions can also include other reagents such as reaction buffers, deoxyribonucleo tides, and reporter molecules such as, for example, fluorophore-modified probe DNAs (e.g., molecular beacon probes) for the fluorescent detection of newly synthesized DNA.
  • reporter molecules generally known in the art can be used, including acridinium conjugated probes (i.e. chemiluminescent technology).
  • the disclosure relates to a kit for detecting a target nucleic acid in a sample, said kit comprising: an oligonucleotide (sequence conversion DNA or SC DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer (PDS) sequence, and a sequence (C) complementary to the 3' end of a target nucleic acid; a polymerase; and an endonuclease for a nicking reaction.
  • an oligonucleotide sequence conversion DNA or SC DNA
  • kits can further comprise a polymerase and/or an endonuclease capable of nicking an endonuclease recognition site or a site adjacent to an endonuclease recognition site.
  • the kits can also include reagents such as reaction buffers, deoxyribonucleotides, and reporter molecules such as, for example, fluorophore-modified probe DNAs (e.g., molecular beacon probes) for the fluorescent detection of newly synthesized DNA such as a signal DNA.
  • the kits can also comprise instructions for use in the practice of any one of the methods disclosed herein.
  • the disclosure relates to a kit for detecting a target nucleic acid in a sample, said kit comprising: a first oligonucleotide (sequence conversion DNA or SC DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer (PDS) sequence, and a sequence (C) complementary to the 3' end of a target nucleic acid; a second oligonucleotide (signal amplifier DNA or SA DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (D) that is homologous to the signal DNA generation sequence (A) of the first oligonucleotide, an endonuclease recognition site (E) (which may be the same or different from the endonuclease recognition site (B) in the SA DNA), a poly DNA spacer (PDS) sequence (which may be the same or different from the
  • the second oligonucleotide or signal amplifier DNA does not have a poly DNA spacer (PDS) sequence.
  • the kits can further comprise a polymerase and/or an endonuclease capable of nicking an endonuclease recognition site or a site adjacent to an endonuclease recognition site.
  • the kits can also include reagents such as reaction buffers, deoxyribonucleotides, and reporter molecules such as, for example, fluorophore- modified probe DNAs (e.g., molecular beacon probes) for the fluorescent detection of newly synthesized DNA such as a signal DNA.
  • the kits can also comprise instructions for use in the practice of any one of the methods disclosed herein.
  • the methods, oligonucleotides, compositions, and kits disclosed herein may be used in combination with integrated system platforms.
  • methods, oligonucleotides, compositions, and kits of the present invention may be used in combination Abbott's ARCHITECT system.
  • the methods, oligonucleotides, compositions, and kits disclosed herein may be used with sample preparation system platforms such as, for example, the m2000sp sample preparation system (Abbott Diagnostics, Abbott Park, IL).
  • the methods, oligonucleotides, compositions, and kits disclosed herein may be used with point-of-care system platforms such as, for example, Abbott's i-STAT point-of-care system (Abbott Diagnostics, Abbott Park, IL). Further, the methods, oligonucleotides, compositions, and kits of the present invention can be used with any number of other devices, assay platforms, and instrumentation such as, for example, hand held fluorescence detectors, micro-pH meters, microfluidic devices, microarrays, enzymatic detection systems, immunochromatographic strips, and lateral flow devices.
  • oligonucleotides, compositions, and kits disclosed herein may be used in the field of molecular diagnostics, including diagnosis of non-infectious and infectious diseases.
  • methods, oligonucleotides, compositions, and kits of the present invention can be used to detect microRNA, messenger RNA, non-coding RNA and methylated DNA in human fluid such as blood, urine, saliva, sweat and feces.
  • methods, oligonucleotides, compositions, and kits of the present invention can be used to detect target nucleic acids originating from infectious diseases such as, for example, HBV, HCV, HIV, HPV, HTLV-I, Parvo virus, Tuberculosis, Syphilis, Malaria and Entamoeba histolytica in human fluid like blood, urine, saliva, sweat and feces.
  • infectious diseases such as, for example, HBV, HCV, HIV, HPV, HTLV-I, Parvo virus, Tuberculosis, Syphilis, Malaria and Entamoeba histolytica in human fluid like blood, urine, saliva, sweat and feces.
  • the SC and SA DNAs disclosed herein may comprise chemically modified nucleotides.
  • the SC and SA DNAs disclosed herein may comprise LNA (Locked Nucleic Acid), BNA (Bridged Nucleic Acid), ENA (Ethylene Bridged Nucleic Acid), GNA (Glycol Nucleic Acid), TNA (Threose Nucleic Acid), PNA (Peptide Nucleic Acid), Morpholino Nucleic Acid, phosphorothioate nucleotides, or combinations and/or derivatives thereof.
  • FIG. 1A is a diagram schematically illustrating a non- limiting example of a Sequence Conversion DNA (SC DNA) for the detection of a target nucleic acid in a sample.
  • the SC DNA comprises, in the 5' to 3' direction, a signal generation sequence (A), an endonuclease recognition site (B) that can be used in a nicking reaction, a poly DNA spacer (PDS) sequence, and a sequence (C) complementary to the target nucleic acid.
  • A signal generation sequence
  • B endonuclease recognition site
  • PDS poly DNA spacer
  • C sequence complementary to the target nucleic acid.
  • FIG. IB is a diagram schematically illustrating a non-limiting example of a Signal Amplifier DNA (SA DNA) for the detection of a target nucleic acid in a sample.
  • the SA DNA comprises, in the 5' to 3' direction, a signal DNA generation sequence (D) homologous to the signal DNA generation sequence (A) of a SC DNA; an endonuclease recognition site (E) (which may be the same or different from the endonuclease recognition site (B) of a SC DNA), a poly DNA spacer (PDS) sequence (that may the same or different from the PDS sequence of a SC DNA), and a sequence (F) that is homologous to the signal DNA generation sequence (A) of a first SC DNA.
  • the signal amplifier DNA (SA DNA) does not have a poly DNA spacer (PDS) sequence.
  • Figure 2A is a diagram schematically illustrating the progression of an exemplary reaction of a target (T) nucleic acid with a Sequence Conversion (SC) DNA for the detection of a target nucleic acid in a sample.
  • Sequences (A)-(C), and the PDS, are as described in Figure 1A, sequence (T) represents a target sequence, sequence (X) represents the sequence produced when Target (T) bound to sequence (C) is extended by polymerase, sequence ( ⁇ ') represents the nicked extension sequence, and sequence (S) represents the signal DNA sequence eventually produced.
  • Figure 2B is a diagram schematically illustrating the progression of an exemplary reaction of a signal DNA (S) with a Signal Amplification (SA) DNA for the detection of a target nucleic acid in a sample.
  • Sequences (D)-(F), and the PDS, are as described in Figure IB
  • sequence (S) is the Signal DNA produced from reaction of Target (T) nucleic acid with SC DNA as described in Figure 2A
  • sequence (Y) represents the sequence produced when Signal DNA (S) bound to sequence (D) is extended by polymerase
  • sequence ( ⁇ ') represents the nicked extension sequence
  • sequence (S) represents the signal DNA sequence eventually produced. Because the SA signal generation sequence (D) is homologous to the SC signal generation sequence (A), the same signal DNA (S) is produced.
  • Figure 3 shows the results of the those reactions performed in Example 1, demonstrating that the presence of a PDS sequence positioned between the endonuclease recognition site (B) and the sequence (C) of a SC DNA accelerates the amplification of signal DNA.
  • Figure 4 shows the results of those reactions performed in Example 2, demonstrating that the presence of a PDS sequence positioned between the endonuclease recognition site (B) and the sequence (C) of a SC DNA enhances nicking of endonuclease recognition site (B).
  • the disclosure relates to nucleic acid constructs that are surprisingly effective in the detection of target nucleic acids in a test sample.
  • the constructs disclosed herein comprise nucleic acid sequences that allow the production of signal DNAs that are generated in the presence of a target nucleic acid, with a concomitant increase in the speed of the reaction.
  • the methods and nucleic acid constructs disclosed herein provide for selective, sensitive, and fast detection of target nucleic acids that may be advantageously performed under low temperature and isothermal conditions.
  • the disclosure relates to an oligonucleotide, which may be referred to herein as a "signal amplifier DNA” (or “SA DNA”) comprising, in the 5' to 3' direction, a first sequence that is complementary to a known signal DNA sequence, an endonuclease recognition site, a poly DNA spacer (PDS) sequence, and a second sequence that is complementary to the same known signal DNA sequence as the first sequence.
  • the first sequence is the signal DNA generation sequence (D) in Figure IB, that is homologous to a known signal DNA generation sequence (A) of a SC DNA.
  • the second sequence is sequence (F) in Figure IB, that is homologous to the same known signal DNA generation sequence (A) of the same SC DNA.
  • the lengths of the first and second sequences may vary, but typically each of the sequences is about the same length as the other. In embodiments, the length of the sequences may be in a range from about 5 to about 100 nucleotides, but are more typically from about 5 to about 30, from about 10 to about 30, or from about 15 to about 30 nucleotides in length.
  • the endonuclease recognition site comprises a sequence that can be recognized, bound, and nicked by an endonuclease as described herein. Such sequences are generally known in the art.
  • the endonuclease recognition site can comprise additional nucleotides either 5' or 3' to the endonuclease binding site (or both 5' and 3') but is typically no more than 10 nucleotides in length.
  • a Sequence Conversion DNA (SC DNA) oligonucleotide for the detection of a target nucleic acid in a sample comprises, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer (PDS) sequence, and a sequence (C) complementary to the 3' end of a target nucleic acid.
  • SC DNA Sequence Conversion DNA
  • a Signal Amplifier DNA (SA DNA) for the detection of a target nucleic acid in a sample comprises, in the 5' to 3' direction, a signal DNA generation sequence (D) homologous to the signal DNA generation sequence (A) of a SC DNA; an endonuclease recognition site (E) (which may be the same or different from an endonuclease recognition site (B) of a SC DNA), a poly DNA spacer (PDS) sequence (which may be the same or different from the PDS of a SC DNA), and a sequence (F) comprising a sequence that is homologous to the signal DNA generation sequence (A) of a SC DNA.
  • the signal amplifier DNA (SA DNA) does not have a poly DNA spacer (PDS) sequence.
  • the SC DNAs disclosed herein comprise a signal generation sequence (A).
  • the signal generation sequence (A) in the SC DNA can comprise any desired nucleic acid sequence and is not limited by any particular sequence.
  • the signal generation sequence (A) provides at least a portion of the template for a signal DNA (e.g., nucleic acid (S) in Figure 2), the production of which indicates the presence of target nucleic acid.
  • the signal generation sequence (A) in the SC DNA is not limited by length. In some embodiments, the signal generation sequence (A) in the SC DNA is from about 5 to about 100 nucleic acid bases, and all integers between 5 and 100.
  • the signal generation sequence (A) in the SC DNA is from about 5 to about 30 nucleic acid bases, and all integers between 5 and 30. In some embodiments, the signal generation sequence (A) in the SC DNA is from about 10 to about 30 nucleic acid bases, and all integers between 10 and 30. In yet further embodiments, the signal generation sequence (A) in the SC DNA is from about 15 to about 30 nucleic acid bases, and all integers between 15 and 30 (e.g., about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29 or about 30 bases).
  • the SA DNAs disclosed herein comprise a signal DNA generation sequence (D) which is homologous to the signal DNA generation sequence (A) of a SC DNA, and a sequence (F) which is homologous to the same signal DNA generation sequence (A) of the same SC DNA.
  • sequences (D) and (F) are completely identical to the corresponding signal DNA generation sequence (A).
  • sequence (F) is identical in sequence to the corresponding signal DNA generation sequence (A) of a SC DNA, except that it is from about 1 to about 5, or from about 1 to about 4, or from about 1 to about 3, or from about 1 to about 2, or 1 base(s) shorter at the 3' end.
  • the signal DNA generation sequence (D) of a SA DNA is homologous to the signal DNA generation sequence (A) of a SC DNA, it follows that the same signal DNA (S) is produced and exponentially amplified.
  • the SC and SA DNAs comprise endonuclease recognition sites (B) and (E) respectively, which can be the same or different.
  • the endonuclease recognition sites (B) and (E) may comprise a sequence that is complementary to a sequence that may be nicked by an endonuclease.
  • the sequence that is nicked by the endonuclease may be within, downstream, or upstream from the sequence that is recognized by the endonuclease.
  • the endonuclease recognition sites (B) and (E) can be recognized by one or more endonucleases present in the reaction, and the endonuclease recognition sites (B) and (E) (or a sequence adjacent to the endonuclease recognition sites (B) and (E)) may be cleaved on only one strand of the double- stranded DNA (i.e. , nicked).
  • binding of a target nucleic acid to the complementary sequence (C) of the SC DNA primes replication via DNA polymerase to create an active, double-stranded form of the endonuclease recognition site (B) that can now serve as a recognition site for an endonuclease ( Figure 2A).
  • Endonuclease nicking at the newly created double-stranded endonuclease site (B), or at a site adjacent to newly created double- stranded endonuclease site (B) then primes replication via DNA polymerase and generates signal DNA (S) (see, e.g., Figure 2A).
  • the endonuclease recognition site (B) is oriented such that the newly replicated strand is nicked, not the SC DNA. That is, when the newly replicated strand is generated the orientation of the endonuclease recognition site in (B) directs endonuclease activity (cleavage) of the newly replicated strand.
  • the endonuclease recognition site comprises a sequence that is complementary to a sequence that is nicked by an endonuclease, allowing the SC oligonucleotide to remain intact throughout the reaction (i.e., the SC DNA is not nicked or cleaved).
  • the SC and SA DNAs can also comprise a poly DNA spacer (PDS) sequence.
  • the PDS sequence is positioned between the endonuclease recognition site (B) and the sequence (C) complementary to the 3' end of the target nucleic acid.
  • the PDS sequence is positioned between the endonuclease recognition site in (E) and the sequence (F) substantially homologous to the signal generation sequence (A) of a SC DNA.
  • the signal amplifier DNA (SA DNA) does not have a poly DNA spacer (PDS) sequence.
  • the PDS sequence of the SC and SA DNAs can be the same or different.
  • the PDS sequence can be comprised of any one or more of the natural bases G, A, T or C, and can be from 3 to 20, from 3 to 18, from 3 to 16, from 3 to 14, from 3 to 14, from 3 to 12, from 3 to 10, from 3 to 8, from 3 to 6, or from 3 to 5 bases long.
  • the presence of a PDS sequence in one or more of the SC or SA DNAs disclosed herein can accelerate reactions performed according to the methods disclosed herein by as much as 5 to 60, 5 to 50, 5 to 40, 5 to 30, 5 to 20, or 5 to 10 minutes.
  • binding of signal DNA (S), generated from the signal generation sequence (A) of a SC DNA, to the sequence (F) of a SA DNA primes replication via DNA polymerase to create an active, double- stranded form of the endonuclease recognition site (E) of the SA DNA that can serve as a recognition site for an endonuclease ( Figure 2B).
  • the endonuclease recognition site (E) is oriented such that the newly replicated strand is nicked, not the SA DNA. That is, when the newly replicated strand is generated the orientation of the endonuclease recognition site in E directs endonuclease activity (cleavage) of the newly replicated strand.
  • the endonuclease recognition site comprises a sequence that is complementary to a sequence that is nicked by an endonuclease, allowing the SA oligonucleotide to remain intact throughout the reaction (i.e., the SA DNA is not nicked or cleaved).
  • the sequence (C) of the SC DNA that is complementary to the target DNA is not limited by length, and can be from about 5 to about 100 nucleic acid bases, and all integers between 5 and 100. In some embodiments, the sequence (C) of the SC DNA is from about 5 to about 30 nucleic acid bases, and all integers between 5 and 30. In some embodiments, the sequence (C) in the SC DNA is from about 10 to about 30 nucleic acid bases, and all integers between 10 and 30. In further embodiments, the sequence (C) of the SC DNA is from about 15 to about 30 nucleic acid bases, and all integers between 15 and 30.
  • Complementary sequences are capable of forming hydrogen bonding interactions to form a double stranded nucleic acid structure (e.g., nucleic acid base pairs).
  • a sequence that is complementary to a first sequence includes a sequence which is capable of forming Watson-Crick base-pairs with the first sequence.
  • the term "complementary" does not require that a sequence is complementary over the full-length of its complementary strand, and encompasses a sequence that is complementary to a portion of another sequence.
  • a complementary sequence encompasses sequences that are complementary over the entire length of the sequence or over a portion thereof (e.g., greater than about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, or about 90% of the length of the sequence).
  • two sequences can be complementary to each other over a length ranging from about 2 to about 100 consecutive (contiguous) nucleotides, or any integer between 2 and 100.
  • two sequences can be complementary to each other over a length ranging from about 15 to about 30 consecutive (contiguous) nucleotides, or any integer between 15 and 30.
  • complementary sequences can encompass sequences that have some sequence mismatches.
  • complementary sequences can include sequences that are complementary to at least about 70% to 100%, preferably greater than above 95% of the length of the sequence. Despite some amount of mismatches, complementary sequences generally have the ability to selectively hybridize to one another under appropriate conditions such as, for example, stringent and highly stringent conditions such as those described herein or generally known by those of ordinary skill in the art.
  • the SC and SA DNAs may be synthesized by known methods.
  • the SC and SA DNAs can be synthesized using a phosphoramidite method, a phosphotriester method, an H-phosphonate method, or a thiophosphonate method.
  • the SC and/or SA DNAs can be purified, for example using ion exchange HPLC.
  • the SC and SA DNAs may comprise chemical modifications such as are generally known in the art.
  • the SC and SA DNAs can comprise chemically modified nucleotides (e.g., 2'-0 methyl derivative, phosphorothioates, etc.), 3' end modifications, 5' end modifications, or any combinations thereof.
  • the 3' end of the SC and SA DNAs may be modified such that an extension reaction does not occur from the 3' end of the SC or SA DNA (e.g., upon binding of a target sequence, or another non-target sequence, that might serve as a primer for polymerase extension).
  • the SC and SA DNAs comprise a 3' end modification that can reduce or eliminate the occurrence of any non-desired extension reactions, such as those discussed above.
  • 3 '-end modifications include TAMRA, DABCYL, and FAM.
  • Other non-limiting examples of modifications include, for example, biotinylation, fluorochromation, phosphorylation, thiolation, amination, inverted nucleotides, or abasic groups.
  • the present invention encompasses methods for detecting a target nucleic acid (T) in a sample.
  • the methods generally comprise contacting said sample with: a first oligonucleotide (or sequence conversion DNA or SC DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (A), an endonuclease recognition site (B), a poly DNA spacer (PDS) sequence, and a sequence (C) which is complementary to the 3' end of said target nucleic acid (T); a second oligonucleotide (or signal amplifier DNA or SA DNA) comprising, in the 5' to 3' direction, a signal DNA generation sequence (D) homologous to the signal DNA generation sequence (A) of the first oligonucleotide, an endonuclease recognition site (E) (which is the same as the endonuclease recognition site (B) of the first oligonucleotide), a poly DNA spacer (PDS) sequence (
  • the method also comprises determining the presence or absence of a signal DNA, wherein the presence of the signal DNA indicates the presence of the target nucleic acid in the sample.
  • the signal amplifier DNA SA DNA
  • PDS poly DNA spacer
  • the method comprises contacting a sample with an endonuclease.
  • the endonuclease may be a nicking endonuclease or a restriction endonuclease that is capable of or that can be used in nicking the sequence complementary to the endonuclease recognition site (B) within the SC DNA, or the sequence complementary to the endonuclease recognition site (E) within the SA DNA.
  • the endonuclease comprises a nicking endonuclease or a restriction endonuclease that can catalyze or can be used to catalyze a double-stranded DNA nicking reaction.
  • the phosphodiester linkage of one strand of a double-strand DNA may be cleaved to generate a phosphate group on the 5 ' side of the cleavage site and a hydroxyl group on the 3 ' side.
  • nicking endonucleases include Nb.BbvCI, NtAlwI, Nt.BbvCI, Nb.BsrDI, Nb.Btsl, Nt.BspQI, Nt.BstNBI, Nb.BsmI, Nt.CviPII, and Nt.BsmAI.
  • the endonuclease may be a restriction endonuclease.
  • the restriction endonuclease recognition site may be modified so that the restriction endonuclease cleaves the phophodiester bond on only one strand of a double stranded DNA, and generates a nick in the double strand.
  • Methods or strategies may be used to modify the activity of the restriction endonuclease such as, for example, including a chemical modification in at least one strand of a double- stranded nucleic acid that is not cleaved by the restriction enzyme.
  • One non-limiting example of such a modification includes replacing the oxygen atom of phosphodiester linkage of one strand with a sulfur atom.
  • the phosphodiester linkage of one strand of a double- strand DNA may be cleaved to generate a phosphate group on the 5' side of the cleavage site and a hydroxyl group on the 3' side.
  • restriction endonucleases include Hinc II, Hind II, Ava I, Fnu4HI, Tthl l ll and Neil.
  • the method comprises contacting a sample with a polymerase.
  • the polymerase may be a DNA polymerase having strand displacement activity.
  • the polymerase may be a polymerase that lacks 5 '-3' exonuclease activity, lacks 3'-5' exonuclease activity, or lacks both 5'-3' and 3'-5' exonuclease activity.
  • the polymerase may be eukaryotic, prokaryotic, or viral in origin, and can also be genetically modified.
  • the polymerase is selected from among those that function at lower temperatures, including ambient (e.g., room) temperatures.
  • Non-limiting examples of DNA polymerases include Klenow fragments, DNA polymerase I derived from E. coli, 5' to 3' exonuclease-deficient Bst DNA polymerases derived from Bacillus stearothermophilus, and 5' to 3' exonuclease-deficient Bca DNA polymerases derived from Bacillus caldotenax.
  • the 3' end sequence of the target nucleic acid (T) hybridizes to the sequence (C) of the SC DNA which is complementary to the target and primes or initiates replication (by the DNA polymerase present in the reaction mixture) thereby generating double stranded extension sequence (X) that includes the double stranded endonuclease recognition site (B).
  • oligonucleotide signal sequence (S) and extension sequence ( ⁇ ') Because the 3'-OH of sequence ( ⁇ ') at the nick serves as an initiation site for subsequent rounds of strand displacement replication, oligonucleotide (S) is displaced from the SC DNA by DNA polymerase which continues to replicate and amplify signal DNA (S) in the reaction mixture.
  • the signal resulting from the production of signal DNA (S) can be further amplified by the presence of a signal amplifier DNA (or SA DNA).
  • signal DNA (S) present in a reaction hybridizes to the sequence (F) of the SA DNA which primes or initiates replication (by the DNA polymerase present in the reaction mixture) thereby generating double stranded extension sequence (Y) that includes the double stranded endonuclease recognition site (E).
  • oligonucleotide signal sequence (S) and extension sequence ( ⁇ ') Because the 3'-OH of sequence ( ⁇ ') at the nick serves as an initiation site for subsequent rounds of strand displacement replication, oligonucleotide (S) is displaced from the SA DNA by DNA polymerase which continues to replicate and amplify signal DNA (S) in the reaction mixture.
  • Methods according to the present invention are useful for the detection of target nucleic acids in a sample.
  • methods of the present invention are useful for the detection of target RNA in a sample.
  • the presence in a SC DNA of a poly DNA spacer (PDS) sequence between the endonuclease recognition site is useful for the detection of target RNA in a sample.
  • PDS poly DNA spacer
  • Methods according to the invention may be performed under isothermal or substantially constant temperature conditions.
  • some fluctuation in temperature is permitted.
  • a substantially constant temperature may fluctuate within a desired or identified target temperature range (e.g., about +/- 2°C or about +/- 5°C).
  • a substantially constant temperature may include temperatures that do not include thermal cycling.
  • methods can be performed at isothermal or substantially constant temperatures such as, for example, (1) temperatures at or below about the calculated/predicted or experimentally determined optimal hybridization or annealing temperature of the target nucleic acid (T) to sequence
  • the methods may comprise reaction temperatures that range from about 20°C to about 70°C, including lower temperatures falling within the range of about 20°C to about 42°C.
  • the reaction temperature range is from 35°C to 40°C (e.g., 35°C, 36°C, 37°C, 38°C, 39°C, or 40°C).
  • the reaction temperature is below 65°C, including lower temperatures below about 55°C, about 50°C, about 45°C, about 40°C, or about 30°C.
  • the methods may be performed for a time that is adequate to allow for amplification of a detectable amount of signal sequence in the presence of a target nucleic acid.
  • the reaction time may range from about 5 minutes to 16 hours, or from about 3 minutes to 16 hours. In still other embodiments, the reaction time may range from about 5 to 120 minutes, or from about 15 to 60 minutes.
  • oligonucleotide (S) is also referred to as a signal DNA (S).
  • S signal DNA
  • the signal DNA (S) is not limited by sequence, and can be any sequence that is amenable to detection.
  • the signal DNA is also not limited by length.
  • the signal DNA can be from about 5 to about 100 bases, and any integer between 5 and 100.
  • the signal DNA can be from about 5 to about 30 nucleic acid bases, and all integers between 5 and 30.
  • the signal DNA can be from about 10 to about 30 bases in length and all integers between 10 and 30.
  • the signal DNA can be from about 15 to about 30 bases in length and all integers between 15 and 30.
  • Methods according to the disclosure may be performed under buffer conditions that comprise a pH range from about 4 to about 10, or from about 7 to about 9.
  • the buffer may comprise a salt concentration from about 10 mM to about 500 mM, or from about 50 mM to 150 mM.
  • the method may be performed using an amount of SC and/or SA DNAs that allows for amplification of a detectable amount of signal sequence in the presence of a target nucleic acid.
  • the SC and/or SA DNA concentration may range from about 100 pM to about 100 ⁇ , from about 1 nM to about 1 ⁇ , from about 5 nM to about 50 nM, or from about 5 nM to about 25 nM.
  • the amplification product can also be detected by using a labeled nucleotide labeled with a biotin, for example.
  • the biotin in the amplification product can be detected using fluorescence-labeled avidin or enzyme-labeled avidin, for example.
  • the amplification product can also be detected with electrodes by using redox intercalator known to those skilled in the art.
  • the amplification product can also be detected using surface plasmon resonance (SPR), a Quarts Crystal Microbalance (QCM), or electrochemical methods (including those methods employing nanopore sensors).
  • the methods according to the present invention detect the presence or absence of a target nucleic acid (T) in a sample.
  • the methods according to the present invention can also be used to quantitatively measure the concentration of a target nucleic acid in a test sample.
  • methods according to the present disclosure can be performed in the presence of a range of different known concentrations of the target nucleic acid, and calibration curves can then be prepared and used as generally practiced in the art.
  • the target nucleic acid ((T) in Figure 2) can comprise any nucleic acid sequence and can include DNA, RNA, chemically modified nucleic acids, non-natural nucleic acids, nucleic acid analogs, or any hybrid or combination thereof.
  • DNA may include cDNA, genomic DNA, and synthetic DNA
  • RNA may include total RNA, mRNA, rRNA, siRNA, hnRNA, piRNA, aRNA, miRNA, and synthetic RNA. While some embodiments relate to particular target nucleic acid sequences, any nucleic acid sequence, including auxiliary nucleic acid sequence, can be a target nucleic acid sequence to be detected. The disclosure provides for the detection of a target nucleic acid with selectivity and sensitivity even when the nucleic acid is a short-chain nucleic acid.
  • sequences (C) of the SC DNA and target nucleic acid (T) allows for specific hybridization between the sequences (e.g., the number of complementary nucleotides in sequence (C) of the sequence conversion DNA and target nucleic acid (T) sequences avoids non-specific hybridization under a given set of reaction conditions).
  • the target nucleic acid sequence can be from, or derived from any number of sources including, for example, genomic DNA, expressed mRNA, nucleic acid sequences from pathogens (microbes, viruses), or therapeutic nucleic acids.
  • the SC and SA DNAs and the methods disclosed herein may be used for the diagnosis and prognosis of diseases (e.g., arising from genetic and infectious sources), identification of contaminants (e.g., food-borne illnesses, equipment contamination), personalized medicine (e.g., monitoring and/or prognosis of a therapy), and the like.
  • molecular diagnostic testing can be performed with respect to the following infectious diseases: Hepatitis B Virus (HBV); hepatitis C (HCV); HCV (genotypes 1 - 6); Human Immunodeficiency Virus type 1 (HIV-1); Chlamydia trachomatis; Neisseria gonorrhoeae; influenza A; influenza B; Respiratory Syncytial Virus (RSV); and Parvo virus.
  • HBV Hepatitis B Virus
  • HCV hepatitis C
  • HCV genotypes 1 - 6
  • HIV-1 Human Immunodeficiency Virus type 1
  • Chlamydia trachomatis Neisseria gonorrhoeae
  • influenza A influenza B
  • RSV Respiratory Syncytial Virus
  • the target nucleic acid can comprise micro-RNAs (miRNA).
  • miRNAs include small non-coding RNA molecules of about 22 nucleotides. Micro-RNAs are known to function in transcription and post-transcriptional regulation of gene expression. It is known that micro-RNAs function by base pairing with complementary regions of messenger RNA (mRNA), resulting in gene silencing via translational repression or target degradation.
  • mRNA messenger RNA
  • sample containing or suspected of containing a target nucleic acid is not specifically limited, and includes, for example, biological samples derived from living subjects, such as whole blood, serum, buffy coat, urine, feces, cerebrospinal fluid, seminal fluid, saliva, tissue (such as cancerous tissue or lymph nodes), cell cultures (such as mammalian cell cultures or bacterial cultures); samples containing nucleic acids, such as viroids, viruses, bacteria, fungi, yeast, plants, and animals; samples (such as food and biological preparations) that may contain or be infected with microorganisms such as viruses or bacteria; and samples that may contain biological substances, such as soil, industrial process and manufacturing equipment, and wastewater; and samples derived from various water sources (e.g., drinking water).
  • biological samples derived from living subjects such as whole blood, serum, buffy coat, urine, feces, cerebrospinal fluid, seminal fluid, saliva, tissue (such as cancerous tissue or lymph nodes), cell cultures (such as mammalian cell
  • a sample may be processed by any known method to prepare a nucleic acid- containing composition used in the methods disclosed herein.
  • preparations can include cell breakage (e.g., cell lysates and extracts), sample fractionation, nucleic acids in the samples, and specific nucleic acid molecular groups such as mRNA-enriched samples.
  • the sample used in the method for detecting a target nucleic acid of the present invention is not limited to those derived from biological and natural products as mentioned above and may be a sample containing a synthetic oligonucleotide.
  • Methods according to the present invention can be performed in combination with the Abbott m2000sp sample preparation system.
  • the m2000sp uses magnetic particle technology to capture nucleic acids and washes the particles to remove unbound sample components.
  • the bound nucleic acids are eluted and transferred to a 96 deep-well plate.
  • the Abbott m2000sp can also combine with the washed nucleic acids transferred to the 96 deep-well plate any reagents required to perform the methods according to the present technology.
  • SC and SA DNAs, polymerases, endonucleases, molecular beacons, and any other reagent e.g., dNTPs
  • Methods according to the present invention can also be interfaced with point-of- care platforms.
  • dNTP deoxyribonucleotide triphosphate
  • the incorporation of a deoxyribonucleotide triphosphate (dNTP) into a growing DNA strand involves the formation of a covalent bond and the release of pyrophosphate and a positively charged hydrogen ion affecting the pH of a reaction.
  • the synthesis of signal DNA according to methods of the present invention can be detected by tracking changes in pH using, for example, point-of-care micro-pH meters.
  • Abbott's i-STAT point-of-care system can be supplied with single-use disposable cartridges containing micro fabricated sensors, calibration solutions, fluidic systems, and waste chambers for analysis of pH.
  • the methods disclosed herein can comprise additional reagents.
  • Some non- limiting examples of other reagents that can be used in the nucleic acid amplification reaction include metallic salts such as sodium chloride, magnesium chloride, magnesium acetate, and magnesium sulfate; substrates such as dNTP mix; and buffer solutions such as Tris-HCl buffer, tricine buffer, sodium phosphate buffer, and potassium phosphate buffer.
  • detergents, oxidants and reducing agents can also be used in the practice of the methods disclosed herein.
  • agents such as dimethyl sulfoxide and betaine (N, N, N-trimethylglycine); acidic substances described in International Publication No.
  • WO 99/54455 and cationic complexes can be used.
  • the methods and nucleic acid structures provided herein may be used in combination with other methods to provide for the exponential amplification of a signal DNA in the presence of a target nucleic acid.
  • the methods and compositions according to the present disclosure may be used in combination with covered sequence conversion DNAs, as described in U.S. Provisional Application 61/927710, entitled “Covered Sequence Conversion DNA and Detection Methods" which is incorporated herein by reference.
  • the term "about” generally refers to a range of numbers that one of skill in the art would consider equivalent to the recited value (i.e., having the same function or result).
  • the term “about”, as used herein, is intended to refer to ranges of approximately 10-20% greater than or less than the referenced value. In certain circumstances, one of skill in the art will recognize that, due to the nature of the referenced value, the term “about” can mean more or less than a 10-20% deviation from that value.
  • the reactions were performed at 37 C in a 25 reaction volume containing New England Biolabs (NEB) Buffer 2 having a final concentration of 10 mM Tris-HCl, 50 mM NaCl, 10 mM MgC12, 1 mM DTT, pH 7.9.
  • the nicking endonuclease used in the reaction was Nb.BbvCI, which was present at a concentration of 0.1 units/ ⁇ .
  • the polymerase used in the reaction was Bst DNA Polymerase Large Fragment, which was present at a concentration of 0.08 units/ ⁇ .
  • the dNTPs were present at a final concentration 200 ⁇ each.
  • a first polymerization reaction was performed at 37 C in a 50 reaction volume containing New England Biolabs (NEB) Buffer 2 having a final concentration of 10 mM Tris-HCl, 50 mM NaCl, 10 mM MgC12, 1 mM DTT, pH 7.9.
  • the polymerase used in the reaction was Bst DNA Polymerase Large Fragment, which was present at a concentration of 0.08 units/ ⁇ .
  • the dNTPs were present at a final concentration 200 ⁇ each. Sequence Conversion DNA was present at 200 nM.
  • Target nucleic acid (DNA #18, RNA # 6, 7, or 8) was present at 200 nM.
  • the polymerization reactions were incubated at 37°C for 10 minutes, followed by incubation at 80°C for 20 minutes, after which reactions were moved to 4°C.

Abstract

Cette invention concerne des procédés permettant de détecter un acide nucléique cible dans un échantillon. Les procédés comprennent la mise en contact dudit échantillon, en présence d'une polymérase et d'une endonucléase, avec un oligonucléotide de conversion de séquence. L'invention concerne également des procédés permettant de détecter un acide nucléique cible dans un échantillon dans lesquels ledit échantillon est mis en contact, en présence d'une polymérase et d'une endonucléase, avec un oligonucléotide de conversion de séquence.et un oligonucléotide amplificateur de signal. Des compositions et des kits comprenant ces oligonucléotides de conversion de séquence et amplificateur de signal sont en outre décrits.
EP15850183.3A 2014-10-14 2015-10-13 Adn de conversion de séquence et amplificateur de signal comportant des séquences espaceurs de poly-adn et procédés de détection l'utilisant Active EP3207159B1 (fr)

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CN107109473A (zh) 2017-08-29
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US20160102345A1 (en) 2016-04-14
US20160102339A1 (en) 2016-04-14
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